rcsb.exdb 1.26__tar.gz → 1.28__tar.gz

{rcsb_exdb-1.26 → rcsb_exdb-1.28}/HISTORY.txt

@@ -108,3 +108,5 @@
                   Update CI/CD to python 3.10
 10-Dec-2024 V1.26 Update PolymerEntityExtractor to sort extracted sequence data;
                   Update Azure pipelines to run on latest macOS and ubuntu version
+23-Jan-2025 V1.27 Update TreeNodeListWorker to index 'id' field
+11-Feb-2025 V1.28 Move ExDB CLI code (workflow, exec, and tests) and Dockerfile to rcsb.workflow to avoid circular imports

{rcsb_exdb-1.26/rcsb.exdb.egg-info → rcsb_exdb-1.28}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: rcsb.exdb
-Version: 1.26
+Version: 1.28
 Summary: RCSB Python ExDB data extraction and loading workflows
 Home-page: https://github.com/rcsb/py-rcsb_exdb
 Author: John Westbrook
@@ -16,29 +16,34 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: OpenEye-toolkits>=2024.1.1
 Requires-Dist: numpy
 Requires-Dist: jsonschema>=2.6.0
 Requires-Dist: rcsb.utils.io>=1.48
-Requires-Dist: rcsb.db>=1.725
-Requires-Dist: rcsb.utils.chem>=0.79
+Requires-Dist: rcsb.db>=1.800
+Requires-Dist: rcsb.utils.chem>=0.81
 Requires-Dist: rcsb.utils.chemref>=0.91
-Requires-Dist: rcsb.utils.citation>=0.22
 Requires-Dist: rcsb.utils.config>=0.40
 Requires-Dist: rcsb.utils.ec>=0.25
 Requires-Dist: rcsb.utils.go>=0.18
 Requires-Dist: rcsb.utils.seq>=0.82
-Requires-Dist: rcsb.utils.seqalign>=0.31
 Requires-Dist: rcsb.utils.targets>=0.82
 Requires-Dist: rcsb.utils.struct>=0.47
 Requires-Dist: rcsb.utils.taxonomy>=0.43
 Requires-Dist: rcsb.utils.dictionary>=1.27
-Requires-Dist: rcsb.workflow>=0.46
-Requires-Dist: statistics; python_version < "3.0"
 Provides-Extra: dev
 Requires-Dist: check-manifest; extra == "dev"
 Provides-Extra: test
 Requires-Dist: coverage; extra == "test"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary
 
 # py-rcsb_exdb
 
@@ -105,57 +110,3 @@ install this system.   Once HomeBrew is installed, you can further install the
 [MongoDB](https://docs.mongodb.com/manual/tutorial/install-mongodb-on-os-x/) packages which
 are required to support the ExDB tools.  HomeBrew also provides a variety of options for
 managing a [Python virtual environments](https://gist.github.com/Geoyi/f55ed54d24cc9ff1c14bd95fac21c042).
-
-### Command Line Interfaces
-
-A convenience CLI `exdb_exec_cli` is provided for performing update and loading operations.
-
-```bash
-exdb_exec_cli --help
-
-usage: exdb_exec_cli [-h] [--data_set_id DATA_SET_ID] [--full] [--etl_chemref]
-                     [--etl_tree_node_lists] [--config_path CONFIG_PATH]
-                     [--config_name CONFIG_NAME] [--db_type DB_TYPE]
-                     [--read_back_check] [--num_proc NUM_PROC]
-                     [--chunk_size CHUNK_SIZE]
-                     [--document_limit DOCUMENT_LIMIT] [--debug] [--mock]
-                     [--cache_path CACHE_PATH] [--rebuild_cache]
-
-optional arguments:
-  -h, --help            show this help message and exit
-  --data_set_id DATA_SET_ID
-                        Data set identifier (default= 2019_14 for current
-                        week)
-  --full                Fresh full load in a new tables/collections (Default)
-  --etl_chemref         ETL integrated chemical reference data
-  --etl_tree_node_lists
-                        ETL tree node lists
-  --config_path CONFIG_PATH
-                        Path to configuration options file
-  --config_name CONFIG_NAME
-                        Configuration section name
-  --db_type DB_TYPE     Database server type (default=mongo)
-  --read_back_check     Perform read back check on all documents
-  --num_proc NUM_PROC   Number of processes to execute (default=2)
-  --chunk_size CHUNK_SIZE
-                        Number of files loaded per process
-  --document_limit DOCUMENT_LIMIT
-                        Load document limit for testing
-  --debug               Turn on verbose logging
-  --mock                Use MOCK repository configuration for testing
-  --cache_path CACHE_PATH
-                        Top cache path for external and local resource files
-  --rebuild_cache       Rebuild cached files from remote resources
-________________________________________________________________________________
-
-```
-
-For example, to construct and load tree nodes list data collections, the following
-command may be used:
-
-```bash
-exdb_exec_cli --mock --full --etl_tree_node_lists --rebuild_cache \
-              --cache_path ./CACHE  \
-              --config_path ./rcsb/mock-data/config/dbload-setup-example.yml \
-              --config_name site_info_configuration >& LOGTREE \
-```

{rcsb_exdb-1.26 → rcsb_exdb-1.28}/README.md

@@ -63,57 +63,3 @@ install this system.   Once HomeBrew is installed, you can further install the
 [MongoDB](https://docs.mongodb.com/manual/tutorial/install-mongodb-on-os-x/) packages which
 are required to support the ExDB tools.  HomeBrew also provides a variety of options for
 managing a [Python virtual environments](https://gist.github.com/Geoyi/f55ed54d24cc9ff1c14bd95fac21c042).
-
-### Command Line Interfaces
-
-A convenience CLI `exdb_exec_cli` is provided for performing update and loading operations.
-
-```bash
-exdb_exec_cli --help
-
-usage: exdb_exec_cli [-h] [--data_set_id DATA_SET_ID] [--full] [--etl_chemref]
-                     [--etl_tree_node_lists] [--config_path CONFIG_PATH]
-                     [--config_name CONFIG_NAME] [--db_type DB_TYPE]
-                     [--read_back_check] [--num_proc NUM_PROC]
-                     [--chunk_size CHUNK_SIZE]
-                     [--document_limit DOCUMENT_LIMIT] [--debug] [--mock]
-                     [--cache_path CACHE_PATH] [--rebuild_cache]
-
-optional arguments:
-  -h, --help            show this help message and exit
-  --data_set_id DATA_SET_ID
-                        Data set identifier (default= 2019_14 for current
-                        week)
-  --full                Fresh full load in a new tables/collections (Default)
-  --etl_chemref         ETL integrated chemical reference data
-  --etl_tree_node_lists
-                        ETL tree node lists
-  --config_path CONFIG_PATH
-                        Path to configuration options file
-  --config_name CONFIG_NAME
-                        Configuration section name
-  --db_type DB_TYPE     Database server type (default=mongo)
-  --read_back_check     Perform read back check on all documents
-  --num_proc NUM_PROC   Number of processes to execute (default=2)
-  --chunk_size CHUNK_SIZE
-                        Number of files loaded per process
-  --document_limit DOCUMENT_LIMIT
-                        Load document limit for testing
-  --debug               Turn on verbose logging
-  --mock                Use MOCK repository configuration for testing
-  --cache_path CACHE_PATH
-                        Top cache path for external and local resource files
-  --rebuild_cache       Rebuild cached files from remote resources
-________________________________________________________________________________
-
-```
-
-For example, to construct and load tree nodes list data collections, the following
-command may be used:
-
-```bash
-exdb_exec_cli --mock --full --etl_tree_node_lists --rebuild_cache \
-              --cache_path ./CACHE  \
-              --config_path ./rcsb/mock-data/config/dbload-setup-example.yml \
-              --config_name site_info_configuration >& LOGTREE \
-```

{rcsb_exdb-1.26 → rcsb_exdb-1.28}/rcsb/exdb/cli/__init__.py

@@ -2,4 +2,4 @@ __docformat__ = "google en"
 __author__ = "John Westbrook"
 __email__ = "john.westbrook@rcsb.org"
 __license__ = "Apache 2.0"
-__version__ = "1.26"
+__version__ = "1.28"

{rcsb_exdb-1.26 → rcsb_exdb-1.28}/rcsb/exdb/tree/TreeNodeListWorker.py

@@ -9,6 +9,7 @@
 # 12-Apr-2023 dwp add CARD ontology tree
 #  8-Aug-2023 dwp Load full (unfiltered) taxonomy tree node list, and stop loading GO tree (will be loaded in DW instead)
 # 27-Aug-2024 dwp Update CARD ontology tree loading
+# 23-Jan-2025 dwp Change indexed field from 'update_id' to 'id'
 #
 ##
 __docformat__ = "google en"
@@ -138,7 +139,7 @@ class TreeNodeListWorker(object):
             # logger.info("GO tree node list length %d", len(nL))
             # if doLoad:
             #     collectionName = "tree_go_node_list"
-            #     ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["update_id"], keyNames=None, addValues=addValues, schemaLevel=None)
+            #     ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["id"], keyNames=None, addValues=addValues, schemaLevel=None)
             #     self.__updateStatus(updateId, databaseName, collectionName, ok, statusStartTimestamp)
             #
             # ---- CATH
@@ -147,7 +148,7 @@ class TreeNodeListWorker(object):
             logger.info("Starting load SCOP node tree length %d", len(nL))
             if doLoad:
                 collectionName = "tree_cath_node_list"
-                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["update_id"], keyNames=None, addValues=addValues, schemaLevel=None)
+                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["id"], keyNames=None, addValues=addValues, schemaLevel=None)
                 self.__updateStatus(updateId, databaseName, collectionName, ok, statusStartTimestamp)
             # ---- SCOP
             scu = ScopClassificationProvider(cachePath=self.__cachePath, useCache=useCache)
@@ -155,7 +156,7 @@ class TreeNodeListWorker(object):
             logger.info("Starting load SCOP node tree length %d", len(nL))
             if doLoad:
                 collectionName = "tree_scop_node_list"
-                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["update_id"], keyNames=None, addValues=addValues, schemaLevel=None)
+                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["id"], keyNames=None, addValues=addValues, schemaLevel=None)
                 self.__updateStatus(updateId, databaseName, collectionName, ok, statusStartTimestamp)
             # --- SCOP2
             scu = Scop2ClassificationProvider(cachePath=self.__cachePath, useCache=useCache)
@@ -163,7 +164,7 @@ class TreeNodeListWorker(object):
             logger.info("Starting load SCOP2 node tree length %d", len(nL))
             if doLoad:
                 collectionName = "tree_scop2_node_list"
-                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["update_id"], keyNames=None, addValues=addValues, schemaLevel=None)
+                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["id"], keyNames=None, addValues=addValues, schemaLevel=None)
                 self.__updateStatus(updateId, databaseName, collectionName, ok, statusStartTimestamp)
             # ---- Ecod
             ecu = EcodClassificationProvider(cachePath=self.__cachePath, useCache=useCache)
@@ -171,7 +172,7 @@ class TreeNodeListWorker(object):
             logger.info("Starting load ECOD node tree length %d", len(nL))
             if doLoad:
                 collectionName = "tree_ecod_node_list"
-                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["update_id"], keyNames=None, addValues=addValues, schemaLevel=None)
+                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["id"], keyNames=None, addValues=addValues, schemaLevel=None)
                 self.__updateStatus(updateId, databaseName, collectionName, ok, statusStartTimestamp)
             # ---- EC
             edbu = EnzymeDatabaseProvider(cachePath=self.__cachePath, useCache=useCache)
@@ -179,7 +180,7 @@ class TreeNodeListWorker(object):
             logger.info("Starting load of EC node tree length %d", len(nL))
             if doLoad:
                 collectionName = "tree_ec_node_list"
-                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["update_id"], keyNames=None, addValues=addValues, schemaLevel=None)
+                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["id"], keyNames=None, addValues=addValues, schemaLevel=None)
                 self.__updateStatus(updateId, databaseName, collectionName, ok, statusStartTimestamp)
             # ---- CARD
             okCou = True
@@ -200,7 +201,7 @@ class TreeNodeListWorker(object):
                         collectionName,
                         loadType=loadType,
                         documentList=nL,
-                        indexAttributeList=["update_id"],
+                        indexAttributeList=["id"],
                         keyNames=None,
                         addValues=addValues,
                         schemaLevel=None
@@ -229,7 +230,7 @@ class TreeNodeListWorker(object):
             if doLoad:
                 collectionName = "tree_taxonomy_node_list"
                 logger.debug("Taxonomy nodes (%d) %r", len(nL), nL[:5])
-                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["update_id"], keyNames=None, addValues=addValues, schemaLevel=None)
+                ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["id"], keyNames=None, addValues=addValues, schemaLevel=None)
                 self.__updateStatus(updateId, databaseName, collectionName, ok, statusStartTimestamp)
             logger.info("Tree loading operations completed.")
             #
@@ -241,7 +242,7 @@ class TreeNodeListWorker(object):
             nL = atcP.getTreeNodeList(filterD=atcFilterD)
             collectionName = "tree_atc_node_list"
             logger.debug("ATC node list length %d %r", len(nL), nL[:5])
-            ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["update_id"], keyNames=None, addValues=addValues, schemaLevel=None)
+            ok = dl.load(databaseName, collectionName, loadType=loadType, documentList=nL, indexAttributeList=["id"], keyNames=None, addValues=addValues, schemaLevel=None)
             self.__updateStatus(updateId, databaseName, collectionName, ok, statusStartTimestamp)
             #
             # ---

{rcsb_exdb-1.26 → rcsb_exdb-1.28/rcsb.exdb.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: rcsb.exdb
-Version: 1.26
+Version: 1.28
 Summary: RCSB Python ExDB data extraction and loading workflows
 Home-page: https://github.com/rcsb/py-rcsb_exdb
 Author: John Westbrook
@@ -16,29 +16,34 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: OpenEye-toolkits>=2024.1.1
 Requires-Dist: numpy
 Requires-Dist: jsonschema>=2.6.0
 Requires-Dist: rcsb.utils.io>=1.48
-Requires-Dist: rcsb.db>=1.725
-Requires-Dist: rcsb.utils.chem>=0.79
+Requires-Dist: rcsb.db>=1.800
+Requires-Dist: rcsb.utils.chem>=0.81
 Requires-Dist: rcsb.utils.chemref>=0.91
-Requires-Dist: rcsb.utils.citation>=0.22
 Requires-Dist: rcsb.utils.config>=0.40
 Requires-Dist: rcsb.utils.ec>=0.25
 Requires-Dist: rcsb.utils.go>=0.18
 Requires-Dist: rcsb.utils.seq>=0.82
-Requires-Dist: rcsb.utils.seqalign>=0.31
 Requires-Dist: rcsb.utils.targets>=0.82
 Requires-Dist: rcsb.utils.struct>=0.47
 Requires-Dist: rcsb.utils.taxonomy>=0.43
 Requires-Dist: rcsb.utils.dictionary>=1.27
-Requires-Dist: rcsb.workflow>=0.46
-Requires-Dist: statistics; python_version < "3.0"
 Provides-Extra: dev
 Requires-Dist: check-manifest; extra == "dev"
 Provides-Extra: test
 Requires-Dist: coverage; extra == "test"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary
 
 # py-rcsb_exdb
 
@@ -105,57 +110,3 @@ install this system.   Once HomeBrew is installed, you can further install the
 [MongoDB](https://docs.mongodb.com/manual/tutorial/install-mongodb-on-os-x/) packages which
 are required to support the ExDB tools.  HomeBrew also provides a variety of options for
 managing a [Python virtual environments](https://gist.github.com/Geoyi/f55ed54d24cc9ff1c14bd95fac21c042).
-
-### Command Line Interfaces
-
-A convenience CLI `exdb_exec_cli` is provided for performing update and loading operations.
-
-```bash
-exdb_exec_cli --help
-
-usage: exdb_exec_cli [-h] [--data_set_id DATA_SET_ID] [--full] [--etl_chemref]
-                     [--etl_tree_node_lists] [--config_path CONFIG_PATH]
-                     [--config_name CONFIG_NAME] [--db_type DB_TYPE]
-                     [--read_back_check] [--num_proc NUM_PROC]
-                     [--chunk_size CHUNK_SIZE]
-                     [--document_limit DOCUMENT_LIMIT] [--debug] [--mock]
-                     [--cache_path CACHE_PATH] [--rebuild_cache]
-
-optional arguments:
-  -h, --help            show this help message and exit
-  --data_set_id DATA_SET_ID
-                        Data set identifier (default= 2019_14 for current
-                        week)
-  --full                Fresh full load in a new tables/collections (Default)
-  --etl_chemref         ETL integrated chemical reference data
-  --etl_tree_node_lists
-                        ETL tree node lists
-  --config_path CONFIG_PATH
-                        Path to configuration options file
-  --config_name CONFIG_NAME
-                        Configuration section name
-  --db_type DB_TYPE     Database server type (default=mongo)
-  --read_back_check     Perform read back check on all documents
-  --num_proc NUM_PROC   Number of processes to execute (default=2)
-  --chunk_size CHUNK_SIZE
-                        Number of files loaded per process
-  --document_limit DOCUMENT_LIMIT
-                        Load document limit for testing
-  --debug               Turn on verbose logging
-  --mock                Use MOCK repository configuration for testing
-  --cache_path CACHE_PATH
-                        Top cache path for external and local resource files
-  --rebuild_cache       Rebuild cached files from remote resources
-________________________________________________________________________________
-
-```
-
-For example, to construct and load tree nodes list data collections, the following
-command may be used:
-
-```bash
-exdb_exec_cli --mock --full --etl_tree_node_lists --rebuild_cache \
-              --cache_path ./CACHE  \
-              --config_path ./rcsb/mock-data/config/dbload-setup-example.yml \
-              --config_name site_info_configuration >& LOGTREE \
-```

{rcsb_exdb-1.26 → rcsb_exdb-1.28}/rcsb.exdb.egg-info/SOURCES.txt

@@ -9,7 +9,6 @@ rcsb/__init__.py
 rcsb.exdb.egg-info/PKG-INFO
 rcsb.exdb.egg-info/SOURCES.txt
 rcsb.exdb.egg-info/dependency_links.txt
-rcsb.exdb.egg-info/entry_points.txt
 rcsb.exdb.egg-info/not-zip-safe
 rcsb.exdb.egg-info/requires.txt
 rcsb.exdb.egg-info/top_level.txt
@@ -29,7 +28,6 @@ rcsb/exdb/citation/CitationAdapter.py
 rcsb/exdb/citation/CitationExtractor.py
 rcsb/exdb/citation/CitationUtils.py
 rcsb/exdb/citation/__init__.py
-rcsb/exdb/cli/ExDbExec.py
 rcsb/exdb/cli/__init__.py
 rcsb/exdb/entry/EntryInfoProvider.py
 rcsb/exdb/entry/__init__.py
@@ -58,7 +56,6 @@ rcsb/exdb/tests/testCitationExtractor.py
 rcsb/exdb/tests/testCitationUtils.py
 rcsb/exdb/tests/testEntryInfoEtlWorkflow.py
 rcsb/exdb/tests/testEntryInfoProvider.py
-rcsb/exdb/tests/testExDbWorkflow.py
 rcsb/exdb/tests/testGlycanEtlWorkflow.py
 rcsb/exdb/tests/testGlycanProvider.py
 rcsb/exdb/tests/testGlycanUtils.py
@@ -89,7 +86,6 @@ rcsb/exdb/utils/ObjectUpdater.py
 rcsb/exdb/utils/ObjectValidator.py
 rcsb/exdb/utils/__init__.py
 rcsb/exdb/wf/EntryInfoEtlWorkflow.py
-rcsb/exdb/wf/ExDbWorkflow.py
 rcsb/exdb/wf/GlycanEtlWorkflow.py
 rcsb/exdb/wf/PubChemEtlWorkflow.py
 rcsb/exdb/wf/__init__.py

{rcsb_exdb-1.26 → rcsb_exdb-1.28}/rcsb.exdb.egg-info/requires.txt

@@ -1,24 +1,17 @@
-OpenEye-toolkits>=2024.1.1
 numpy
 jsonschema>=2.6.0
 rcsb.utils.io>=1.48
-rcsb.db>=1.725
-rcsb.utils.chem>=0.79
+rcsb.db>=1.800
+rcsb.utils.chem>=0.81
 rcsb.utils.chemref>=0.91
-rcsb.utils.citation>=0.22
 rcsb.utils.config>=0.40
 rcsb.utils.ec>=0.25
 rcsb.utils.go>=0.18
 rcsb.utils.seq>=0.82
-rcsb.utils.seqalign>=0.31
 rcsb.utils.targets>=0.82
 rcsb.utils.struct>=0.47
 rcsb.utils.taxonomy>=0.43
 rcsb.utils.dictionary>=1.27
-rcsb.workflow>=0.46
-
-[:python_version < "3.0"]
-statistics
 
 [dev]
 check-manifest

{rcsb_exdb-1.26 → rcsb_exdb-1.28}/requirements.txt

@@ -1,20 +1,17 @@
 --extra-index-url https://pypi.anaconda.org/OpenEye/simple
-OpenEye-toolkits >= 2024.1.1
+# Above line may be needed despite the OpenEye package not being a direct requirement of this package (it's used by rcsb.utils.chem)
+# OpenEye-toolkits >= 2024.1.1
 numpy
 jsonschema >= 2.6.0
 rcsb.utils.io >= 1.48
-rcsb.db >= 1.725
-rcsb.utils.chem >= 0.79
+rcsb.db >= 1.800
+rcsb.utils.chem >= 0.81
 rcsb.utils.chemref >= 0.91
-rcsb.utils.citation >= 0.22
 rcsb.utils.config >= 0.40
 rcsb.utils.ec >= 0.25
 rcsb.utils.go >= 0.18
 rcsb.utils.seq >= 0.82
-rcsb.utils.seqalign >= 0.31
 rcsb.utils.targets >= 0.82
 rcsb.utils.struct >= 0.47
 rcsb.utils.taxonomy >= 0.43
 rcsb.utils.dictionary >= 1.27
-rcsb.workflow >= 0.46
-statistics; python_version < "3.0"

{rcsb_exdb-1.26 → rcsb_exdb-1.28}/setup.py

@@ -47,7 +47,6 @@ setup(
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
     ],
-    entry_points={"console_scripts": ["exdb_exec_cli=rcsb.exdb.cli.ExDbExec:main"]},
     #
     install_requires=packagesRequired[1:],
     packages=find_packages(exclude=["rcsb.mock-data", "rcsb.exdb.tests-anal", "rcsb.exdb.tests-*", "tests.*"]),
@@ -57,7 +56,7 @@ setup(
     },
     #
     test_suite="rcsb.exdb.tests",
-    tests_require=["tox"],
+    tests_require=["tox", "rcsb.utils.citation >= 0.22"],
     #
     # Not configured ...
     extras_require={"dev": ["check-manifest"], "test": ["coverage"]},